USDA-ARS-BEAR, Richard J. Russell Research Center, P.O. Box 5677, Athens, GA 30604-5677, USA.
Appl Environ Microbiol. 2011 Oct;77(19):6991-9. doi: 10.1128/AEM.00567-11. Epub 2011 Aug 12.
In the family Enterobacteriaceae, plasmids have been classified according to 27 incompatibility (Inc) or replicon types that are based on the inability of different plasmids with the same replication mechanism to coexist in the same cell. Certain replicon types such as IncA/C are associated with multidrug resistance (MDR). We developed a microarray that contains 286 unique 70-mer oligonucleotide probes based on sequences from five IncA/C plasmids: pYR1 (Yersinia ruckeri), pPIP1202 (Yersinia pestis), pP99-018 (Photobacterium damselae), pSN254 (Salmonella enterica serovar Newport), and pP91278 (Photobacterium damselae). DNA from 59 Salmonella enterica isolates was hybridized to the microarray and analyzed for the presence or absence of genes. These isolates represented 17 serovars from 14 different animal hosts and from different geographical regions in the United States. Qualitative cluster analysis was performed using CLUSTER 3.0 to group microarray hybridization results. We found that IncA/C plasmids occurred in two lineages distinguished by a major insertion-deletion (indel) region that contains genes encoding mostly hypothetical proteins. The most variable genes were represented by transposon-associated genes as well as four antimicrobial resistance genes (aphA, merP, merA, and aadA). Sixteen mercury resistance genes were identified and highly conserved, suggesting that mercury ion-related exposure is a stronger pressure than anticipated. We used these data to construct a core IncA/C genome and an accessory genome. The results of our studies suggest that the transfer of antimicrobial resistance determinants by transfer of IncA/C plasmids is somewhat less common than exchange within the plasmids orchestrated by transposable elements, such as transposons, integrating and conjugative elements (ICEs), and insertion sequence common regions (ISCRs), and thus pose less opportunity for exchange of antimicrobial resistance.
在肠杆菌科家族中，质粒根据 27 种不相容性（Inc）或复制子类型进行分类，这些类型基于具有相同复制机制的不同质粒不能共存于同一细胞。某些复制子类型，如 IncA/C，与多药耐药性（MDR）有关。我们开发了一种微阵列，其中包含基于五个 IncA/C 质粒（Yersinia ruckeri 的 pYR1、Yersinia pestis 的 pPIP1202、Photobacterium damselae 的 pP99-018、Salmonella enterica serovar Newport 的 pSN254 和 Photobacterium damselae 的 pP91278）序列的 286 个独特的 70 -mer 寡核苷酸探针。将 59 个沙门氏菌属分离株的 DNA 杂交到微阵列上，并分析是否存在基因。这些分离株代表了来自 14 个不同动物宿主和美国不同地理区域的 17 个血清型。使用 CLUSTER 3.0 进行定性聚类分析，对微阵列杂交结果进行分组。我们发现 IncA/C 质粒存在于两个谱系中，它们通过一个主要的插入-缺失（indel）区域区分开来，该区域包含编码大多假设蛋白的基因。最易变的基因由转座子相关基因以及四个抗微生物药物抗性基因（aphA、merP、merA 和 aadA）代表。鉴定出 16 个汞抗性基因，高度保守，表明汞离子相关暴露的压力比预期的要大。我们使用这些数据构建了核心 IncA/C 基因组和辅助基因组。研究结果表明，IncA/C 质粒介导的抗微生物药物抗性决定因素的转移不如转座元件（如转座子、整合和共轭元件（ICEs）以及插入序列共同区域（ISCRs））在质粒内部协调的交换常见，因此抗微生物药物抗性的交换机会较少。
